Alternatives and similar repositories for epiphany

Users that are interested in epiphany are comparing it to the libraries listed below

• mdozmorov / scHiC_notes
  Notes on single-cell Hi-C technologies, tools, and data
  ☆84Updated last year
• ma-compbio / Higashi
  single-cell Hi-C, scHi-C, Hi-C, 3D genome, nuclear organization, hypergraph
  ☆91Updated 2 weeks ago
• jzhoulab / orca
  sequence-based prediction of multiscale genome structure from kilobase to whole-chromosome scale
  ☆93Updated 8 months ago
• VRam142 / combinatorialHiC
  Scripts + resources for analyzing combinatorial Hi-C data
  ☆31Updated 6 years ago
• FunctionLab / sei-framework
  code to run sei and obtain sei and sequence class predictions
  ☆109Updated 2 years ago
• calico / scBasset
  Sequence-based Modeling of single-cell ATAC-seq using Convolutional Neural Networks.
  ☆98Updated 2 months ago
• jzhoulab / puffin
  deep learning-inspired explainable sequence model for transcription initiation
  ☆98Updated 8 months ago
• tanjimin / C.Origami
  C.Origami, a prediction and screening framework for cell type-specific 3D chromatin structure.
  ☆81Updated last year
• kundajelab / chrombpnet
  Bias factorized, base-resolution deep learning models of chromatin accessibility (chromBPNet)
  ☆186Updated 2 months ago
• ketringjoni / SuPreMo
  Pipeline for generating reference and perturbed sequences for input into predictive models.
  ☆11Updated last year
• zhoujt1994 / scHiCluster
  ☆68Updated 5 months ago
• JinLabBioinfo / HiCorr
  HiCorr: a Hi-C data bias-correction pipeline
  ☆29Updated 7 months ago
• jsxlei / SCALE
  Single-cell ATAC-seq analysis via Latent feature Extraction
  ☆103Updated 2 years ago
• buenrostrolab / scPrinter
  ☆54Updated last month
• tanlongzhi / dip-c
  Tools to analyze Dip-C (or other 3C/Hi-C) data
  ☆72Updated last year
• YeoLab / eCLIP
  ☆38Updated 3 years ago
• satijalab / PASTA
  ☆21Updated last year
• dylkot / pyWNN
  Weighted Nearest Neighbors Analysis implemented in Python (pyWNN)
  ☆19Updated 4 years ago
• xryanglab / RiboMiner
  a toolset for mining multi-dimensional features of the translatome with ribosome profiling data
  ☆18Updated 3 months ago
• MonashBioinformaticsPlatform / polyApipe
  polyApipe
  ☆19Updated 9 months ago
• liu-bioinfo-lab / EPCOT
  ☆24Updated 2 years ago
• gao-lab / Cell_BLAST
  A BLAST-like toolkit for large-scale scRNA-seq data querying and annotation.
  ☆94Updated last year
• yal054 / epiformer
  ☆26Updated 7 months ago
• GET-Foundation / get_model
  A modular framework for multimodal cross-cell-type transcriptional regulation models
  ☆93Updated 3 months ago
• pinellolab / EPInformer
  code to run EPInformer for gene expression prediction and gene-enhancer link prediction
  ☆43Updated last month
• zhaoweiyu-github / ChromBERT
  ChromBERT: A pre-trained foundation model for context-specific transcription regulatory network
  ☆16Updated last month
• dejunlin / hicrep
  Python implementation of HiCRep stratum-adjusted correlation coefficient of Hi-C data with Cooler sparse contact matrix support
  ☆39Updated last year
• xryanglab / SCASL
  single-cell clustering based on alternative splicing landscapes
  ☆23Updated last year
• Hughes-Genome-Group / deepC
  A neural network framework for predicting the Hi-C chromatin interactions from megabase scale DNA sequence
  ☆33Updated last year
• lrylaarsdam / amethyst
  A comprehensive toolkit for single-cell methylation sequencing data analysis
  ☆28Updated 3 weeks ago